NOC3L

NOC3 like DNA replication regulator, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 10:94333225-94362959

Previous symbols: [ "C10orf117" ]

Links

ENSG00000173145 ∙ NCBI:64318 ∙ OMIM:610769 ∙ HGNC:24034 ∙ Uniprot:Q8WTT2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NOC3L gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOC3L gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in NOC3L

This is a list of pathogenic ClinVar variants found in the NOC3L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-94334238-C-T		not specified	Likely benign (Apr 07, 2022)
10-94334687-T-C		not specified	Uncertain significance (Sep 29, 2022)
10-94334701-A-G		not specified	Uncertain significance (Mar 13, 2023)
10-94334716-G-A		not specified	Uncertain significance (Jan 27, 2022)
10-94337780-C-T		not specified	Uncertain significance (Dec 03, 2021)
10-94338631-G-T		not specified	Uncertain significance (Dec 14, 2021)
10-94338676-G-T		not specified	Uncertain significance (Aug 08, 2022)
10-94339828-C-T		not specified	Uncertain significance (Jun 23, 2023)
10-94340279-C-T		not specified	Uncertain significance (Aug 01, 2022)
10-94344449-G-A		not specified	Uncertain significance (Sep 29, 2023)
10-94344509-C-G		not specified	Uncertain significance (Oct 26, 2022)
10-94349362-C-T		not specified	Uncertain significance (Oct 20, 2023)
10-94350203-C-G		not specified	Uncertain significance (Apr 05, 2023)
10-94350231-C-A		not specified	Uncertain significance (Jun 03, 2022)
10-94352400-G-C		not specified	Uncertain significance (Jan 31, 2023)
10-94352403-T-A		not specified	Uncertain significance (Dec 28, 2023)
10-94352948-A-G		not specified	Uncertain significance (Jul 19, 2023)
10-94352963-T-A		not specified	Uncertain significance (Dec 27, 2023)
10-94353021-C-T		not specified	Uncertain significance (Dec 12, 2023)
10-94353025-C-G		not specified	Uncertain significance (Dec 07, 2021)
10-94353030-T-C		not specified	Uncertain significance (Jan 10, 2022)
10-94353042-C-G		not specified	Uncertain significance (Nov 28, 2023)
10-94355023-C-G		not specified	Uncertain significance (Oct 13, 2023)
10-94355036-T-C		not specified	Uncertain significance (Sep 27, 2021)
10-94356570-T-A		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOC3L	protein_coding	protein_coding	ENST00000371361	21	47713

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.83e-14	0.963	125397	0	351	125748	0.00140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.446	371	396	0.937	0.0000193	5249
Missense in Polyphen		90	108.95	0.82609		1449
Synonymous	-0.107	136	134	1.01	0.00000621	1438
Loss of Function	2.34	29	46.1	0.629	0.00000250	588

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00106
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000851	0.000816
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00236	0.00235
Middle Eastern	0.000851	0.000816
South Asian	0.00103	0.00101
Other	0.00151	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required for adipogenesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• loftool: 0.952
• rvis_EVS: 2.14
• rvis_percentile_EVS: 97.95

Haploinsufficiency Scores

• pHI: 0.382
• hipred: Y
• hipred_score: 0.607
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.312

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Noc3l
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: noc3l
• Affected structure: neutrophil
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;fat cell differentiation
• Cellular component: nucleus;nucleolus;mitochondrion;nuclear speck
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;RNA binding